Protein profile

KP13_00862

Histidyl-tRNA synthetase

Genome: KpKP13

Gene: hisS AHE43225.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3H1G0

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Amino acids 424

Annotations 5

Features 27

PDB binders 3

Druggability 0.645

Overview

Basic information about this protein and its source genome.

Accession: KP13_00862
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: hisS AHE43225.1
Status: annotated
Amino acids: 424
Structure source: AlphaFold + ColabFold

6.1.1.21

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0004821 Catalysis of the reaction: ATP + L-histidine + tRNA(His) = AMP + diphosphate + L-histidyl-tRNA(His). GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0006427 The process of coupling histidine to histidyl-tRNA, catalyzed by histidyl-tRNA synthetase. The histidyl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3''-OH group of a histidine-accetping tRNA.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 25.269
Human E-value: 6.26e-11
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 91.509
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 94.93

Selected Druggability evidence

AlphaFold / UniProt model

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.645

Structure A0A0H3H1G0

Pocket Pocket 6

P2Rank 0.87

Structure A0A0H3H1G0

Pocket Pocket 1

ColabFold model

FPocket 0.375 · Pocket 15

P2Rank 0.835 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 266 / 4744 genomes with a hit

Normalized 0.056

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

6.1.1.21

Gene Ontology (GO)

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0004821 Catalysis of the reaction: ATP + L-histidine + tRNA(His) = AMP + diphosphate + L-histidyl-tRNA(His).
GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO:0006427 The process of coupling histidine to histidyl-tRNA, catalyzed by histidyl-tRNA synthetase. The histidyl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3''-OH group of a histidine-accetping tRNA.

Sequence Features

Domain/signature hits from InterPro and related databases.

27 records

Show feature table

Start	End	DB	Term	Name
328	420	CDD	cd00859	HisRS_anticodon
328	420	InterPro	IPR033656	Histidyl-anticodon-binding
326	423	Gene3D	G3DSA:3.40.50.800	-
326	423	InterPro	IPR036621	Anticodon-binding domain superfamily
18	317	CDD	cd00773	HisRS-like_core
18	317	InterPro	IPR041715	Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain
2	323	FunFam	G3DSA:3.30.930.10:FF:000005	Histidine--tRNA ligase
5	318	SUPERFAMILY	SSF55681	Class II aaRS and biotin synthetases
5	318	InterPro	IPR045864	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
10	312	Pfam	PF13393	Histidyl-tRNA synthetase
10	312	InterPro	IPR041715	Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain
326	423	FunFam	G3DSA:3.40.50.800:FF:000007	Histidine--tRNA ligase
338	420	Pfam	PF03129	Anticodon binding domain
338	420	InterPro	IPR004154	Anticodon-binding
1	423	PIRSF	PIRSF001549	His-tRNA_synth
1	423	InterPro	IPR004516	Histidine-tRNA ligase/ATP phosphoribosyltransferase regulatory subunit
2	322	Gene3D	G3DSA:3.30.930.10	Bira Bifunctional Protein; Domain 2
2	322	InterPro	IPR045864	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
329	423	SUPERFAMILY	SSF52954	Class II aaRS ABD-related
4	414	PANTHER	PTHR43707	HISTIDYL-TRNA SYNTHETASE
4	414	InterPro	IPR004516	Histidine-tRNA ligase/ATP phosphoribosyltransferase regulatory subunit
6	411	NCBIfam	TIGR00442	histidine--tRNA ligase
6	411	InterPro	IPR015807	Histidine-tRNA ligase
1	327	ProSiteProfiles	PS50862	Aminoacyl-transfer RNA synthetases class-II family profile.
1	327	InterPro	IPR006195	Aminoacyl-tRNA synthetase, class II
3	421	Hamap	MF_00127	Histidine--tRNA ligase [hisS].
3	421	InterPro	IPR015807	Histidine-tRNA ligase

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

Loading 3D structure...

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Structural evidence

0 + 2

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold AF_A0A0H3H1G0	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_00862	ColabFold	—	—	full sequence	—	Loaded

Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET	Sticks	Spheres	Surfaces	Druggability	Labels	Zoom	Positions
6				0.645
22				0.357

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				16.77	0.787
2				1.53	0.023

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET	Sticks	Spheres	Surfaces	Druggability	Labels	Zoom	Positions
15				0.375
13				0.219

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Score	Probability
1	13.29	0.681
2	1.63	0.027
3	0.95	0.005

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

53 records

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, use Open crystal to inspect it in the structure viewer.

No PDB structure with a co-crystallized ligand found for this exact protein.

Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.

Ligand	Source crystal	UniProt (homolog)	MW · LogP · TPSA	Lipinski	PAINS	SMILES
HAM	1KMM	P60906	484.4 Da LogP -3.37 TPSA 251.3	1 viol.	✓ Clean	`c1c(nc[nH]1)C[C@@H](C(=O)O[P@](=O)([O-])OC[C@@H…`
HSO	1KMN	P60906	142.2 Da LogP -1.31 TPSA 76.2	✓ Ro5	✓ Clean	`c1c([nH+]c[nH]1)C[C@@H](CO)N`
HSS	2EL9	P60906	483.5 Da LogP -3.30 TPSA 246.5	2 viol.	✓ Clean	`c1c([nH]cn1)C[C@@H](C(=O)NS(=O)(=O)OC[C@@H]2[C@…`

Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL bioactivity data found for this exact protein.

Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL hits found through similar proteins.

Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).

Ligand	Tanimoto	MW · LogP · TPSA	Lipinski	PAINS	SMILES
ZINC1083817667	0.716	459.5 Da LogP -2.22 TPSA 217.8	1 viol.	✓ Clean	`CC(C)C[C@@H](N)C(=O)NS(=O)(=O)OC[C@H]1O[C@@H](n…`
ZINC936069053	0.716	459.5 Da LogP -2.22 TPSA 217.8	1 viol.	✓ Clean	`CC(C)C[C@@H](N)C(=O)NS(=O)(=O)OC[C@@H]1O[C@H](n…`
ZINC168710640	0.707	474.5 Da LogP -4.00 TPSA 260.9	2 viol.	✓ Clean	`NC(=O)CC[C@H](N)C(=O)NS(=O)(=O)OC[C@H]1O[C@@H](…`
ZINC168710738	0.707	474.5 Da LogP -4.00 TPSA 260.9	2 viol.	✓ Clean	`NC(=O)CC[C@H](N)C(=O)NS(=O)(=O)OC[C@H]1O[C@@H](…`
ZINC936069043	0.671	459.5 Da LogP -2.22 TPSA 217.8	1 viol.	✓ Clean	`CC[C@@H](C)[C@@H](N)C(=O)NS(=O)(=O)OC[C@@H]1O[C…`
ZINC14967098	0.658	403.4 Da LogP -3.64 TPSA 217.8	1 viol.	✓ Clean	`NCC(=O)NS(=O)(=O)OC[C@H]1O[C@@H](n2cnc3c(N)ncnc…`
ZINC218033334	0.658	403.4 Da LogP -3.64 TPSA 217.8	1 viol.	✓ Clean	`NCC(=O)NS(=O)(=O)OC[C@H]1O[C@@H](n2cnc3c(N)ncnc…`
ZINC218033425	0.658	403.4 Da LogP -3.64 TPSA 217.8	1 viol.	✓ Clean	`NCC(=O)NS(=O)(=O)OC[C@H]1O[C@@H](n2cnc3c(N)ncnc…`
ZINC218033503	0.658	403.4 Da LogP -3.64 TPSA 217.8	1 viol.	✓ Clean	`NCC(=O)NS(=O)(=O)OC[C@H]1O[C@@H](n2cnc3c(N)ncnc…`
ZINC12405780	0.600	346.3 Da LogP -2.75 TPSA 188.7	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COS(N)(=O)=O)[C@@H]…`
ZINC12502832	0.600	346.3 Da LogP -2.75 TPSA 188.7	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COS(N)(=O)=O)[C@@H]…`
ZINC79460727	0.600	346.3 Da LogP -2.75 TPSA 188.7	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COS(N)(=O)=O)[C@H](…`
ZINC79460732	0.600	346.3 Da LogP -2.75 TPSA 188.7	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COS(N)(=O)=O)[C@H](…`
ZINC31475423	0.592	434.3 Da LogP -2.99 TPSA 238.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO[P@@](=O)(O)OC(=O)…`
ZINC105372833	0.592	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@H](O…`
ZINC105372837	0.592	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@H](O…`
ZINC13518964	0.592	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC1532515	0.592	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@H](O…`
ZINC1571045	0.592	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC17107643	0.592	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@@H](…`
ZINC1842158	0.592	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@H](O…`
ZINC204538551	0.592	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@@H](…`
ZINC2046931	0.592	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC2126310	0.592	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3201891	0.592	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC3201893	0.592	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3830180	0.592	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3860156	0.592	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3977897	0.592	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](COP(=O)(O)O)[C@@H](O…`
ZINC4806442	0.592	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC8613167	0.592	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC4096224	0.583	346.2 Da LogP -1.90 TPSA 191.9	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](N)(=O)O)[C@@…`
ZINC14967079	0.582	461.4 Da LogP -2.95 TPSA 258.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COS(=O)(=O)/N=C(\O)…`
ZINC31516918	0.570	446.4 Da LogP -1.33 TPSA 218.2	1 viol.	✓ Clean	`CC(C)[C@H](N)C(=O)O[P@](=O)(O)OC[C@H]1O[C@@H](n…`
ZINC5615251	0.568	375.3 Da LogP -0.55 TPSA 164.1	1 viol.	✓ Clean	`COP(=O)(OC)OC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@…`
ZINC5615253	0.568	375.3 Da LogP -0.55 TPSA 164.1	1 viol.	✓ Clean	`COP(=O)(OC)OC[C@@H]1O[C@@H](n2cnc3c(N)ncnc32)[C…`
ZINC5615258	0.568	375.3 Da LogP -0.55 TPSA 164.1	1 viol.	✓ Clean	`COP(=O)(OC)OC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@…`
ZINC5615263	0.568	375.3 Da LogP -0.55 TPSA 164.1	1 viol.	✓ Clean	`COP(=O)(OC)OC[C@@H]1O[C@@H](n2cnc3c(N)ncnc32)[C…`
ZINC31539924	0.561	494.4 Da LogP -0.74 TPSA 218.2	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OC(=O…`
ZINC105469665	0.560	425.2 Da LogP -1.64 TPSA 223.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)CP(=O…`
ZINC12360002	0.560	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC13527614	0.560	425.2 Da LogP -1.64 TPSA 223.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)CP(=O)…`
ZINC1582675	0.560	403.3 Da LogP 0.23 TPSA 164.1	1 viol.	✓ Clean	`CCOP(=O)(OCC)OC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[…`
ZINC219330894	0.560	425.2 Da LogP -1.64 TPSA 223.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)CP(=O)…`
ZINC31977053	0.560	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)OP(=O)…`
ZINC3873853	0.560	425.2 Da LogP -1.64 TPSA 223.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@](=O)(O)CP(=O…`
ZINC53683898	0.560	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC5486730	0.560	403.3 Da LogP 0.23 TPSA 164.1	1 viol.	✓ Clean	`CCOP(=O)(OCC)OC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[…`
ZINC5486734	0.560	403.3 Da LogP 0.23 TPSA 164.1	1 viol.	✓ Clean	`CCOP(=O)(OCC)OC[C@@H]1O[C@@H](n2cnc3c(N)ncnc32)…`
ZINC8586019	0.560	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)OP(=O)…`

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.